BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 020252
(328 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB
PE=2 SV=2
Length = 572
Score = 294 bits (752), Expect = 6e-79, Method: Compositional matrix adjust.
Identities = 188/324 (58%), Positives = 233/324 (71%), Gaps = 16/324 (4%)
Query: 1 MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
+T++LDV KLRLPS + S+++ ++RQWTY GPSTE +LA+ETL TSDEAV+
Sbjct: 49 LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108
Query: 60 AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
AA+AEAVALARAAVKVAKDA L N +N+ ++SS S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGI 162
Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTE 173
+G D+ IV S ++ + DLE +E L E+ S S+AVRS RQTE
Sbjct: 163 LGHLAVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTE 219
Query: 174 RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
RKARR + EK A+ + SVK+GS+ ++KR QEVD++DPLRYLR TTSSS+LLT EE
Sbjct: 220 RKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279
Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
+LSAGIQDLLKLE L+ L+ER G PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI S
Sbjct: 280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339
Query: 294 NIRLVISIAKNYQGAGMNLQDLVQ 317
NIRLVISIAKNYQGAGMNLQDLVQ
Sbjct: 340 NIRLVISIAKNYQGAGMNLQDLVQ 363
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis
thaliana GN=SIGF PE=1 SV=1
Length = 547
Score = 102 bits (253), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 59/152 (38%), Positives = 87/152 (57%), Gaps = 1/152 (0%)
Query: 166 VRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSR 225
VRS+RQ ER+A+ RA + + TS +K+ Q D D L+ + +
Sbjct: 188 VRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYK-QGADNDDALQLFLWGPETKQ 246
Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
LLTA EE +L + IQ LLKLE ++ L + G PT +WA A G+ L+ ++ G
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306
Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
++K+IT+N+RLV+ IAK YQ G+N QDL+Q
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338
>sp|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 /
UTEX 2576) GN=rpoD PE=3 SV=1
Length = 390
Score = 91.7 bits (226), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 54/127 (42%), Positives = 76/127 (59%), Gaps = 2/127 (1%)
Query: 193 KSG--STSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE 250
KSG + SRR+ S ++ D +R RLL A+EE++L+ I DLL+LE +RE
Sbjct: 59 KSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRE 118
Query: 251 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM 310
LSE+ P ++WA A + R RL+ G KDKM+ SN+RLV+SIAK Y G+
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGL 178
Query: 311 NLQDLVQ 317
+ QDL+Q
Sbjct: 179 SFQDLIQ 185
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD1 PE=3 SV=2
Length = 399
Score = 79.0 bits (193), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 49/106 (46%), Positives = 65/106 (61%)
Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 271
D +R RLL A+EE++L+ I DLL LE +R+ L E+ P+ A+WAAA
Sbjct: 89 DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148
Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
E RRRL G KDKM+ SN+RLV+SIAK Y G++ QDL+Q
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 194
>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD3 PE=3 SV=1
Length = 320
Score = 74.3 bits (181), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 49/113 (43%), Positives = 67/113 (59%), Gaps = 3/113 (2%)
Query: 207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQ 264
E SD +R YLR LLT EE+ L +Q +KL+ LR+ L SE P+ +
Sbjct: 5 ETPTSDLVRTYLREIGRVP-LLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLE 63
Query: 265 WAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
WAAAAG+ ELR++ + G K KMI +N+RLV+S+AK Y M+L DL+Q
Sbjct: 64 WAAAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQ 116
>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD2 PE=1 SV=1
Length = 320
Score = 72.8 bits (177), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 39/93 (41%), Positives = 55/93 (59%)
Query: 225 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 284
RLLTA EE+ +Q L+ L + L +R G P+ +WAAA ++ +L R++ G
Sbjct: 24 RLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLDRQIEQGQ 83
Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
K KMI +N+RLV+SIAK YQ M DL+Q
Sbjct: 84 RAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQ 116
>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC
PE=2 SV=1
Length = 571
Score = 72.8 bits (177), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/86 (37%), Positives = 57/86 (66%)
Query: 232 EMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291
E ++S G++ + +E +R L E G + + WAAAAG++++ L R L+YG C+D+++
Sbjct: 278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELV 337
Query: 292 TSNIRLVISIAKNYQGAGMNLQDLVQ 317
S LV+ +A+NY+G G+ +DL+Q
Sbjct: 338 KSTRSLVLFLARNYRGLGIAHEDLIQ 363
>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa
GN=rpoD1 PE=3 SV=1
Length = 416
Score = 66.2 bits (160), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 46/145 (31%), Positives = 63/145 (43%), Gaps = 39/145 (26%)
Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE--------------VLSERCG 257
D +R RLL A EE++L+ I DLLKLE +RE L ER
Sbjct: 67 DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126
Query: 258 G-------------------------SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 292
+P +W A + +RRL +G K+KM+
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186
Query: 293 SNIRLVISIAKNYQGAGMNLQDLVQ 317
SN+RLV+SIAK Y G++ QDL+Q
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQ 211
>sp|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX
2576) GN=sigB PE=3 SV=1
Length = 332
Score = 61.2 bits (147), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 56/96 (58%)
Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
LL+ +E+ + +Q ++ + +E L+E+ PT +WA + + L ++L+ G +
Sbjct: 37 LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96
Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQAL 321
K KMI +N+RLV+SIAK YQ + DL+Q AL
Sbjct: 97 AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGAL 132
>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA
PE=1 SV=1
Length = 502
Score = 55.8 bits (133), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 44/143 (30%), Positives = 72/143 (50%), Gaps = 12/143 (8%)
Query: 176 ARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQ 234
AR+ R K N+ VK+ V +V +R Y++ S +L+ E ++
Sbjct: 159 ARQRRIGAKKKTNMTHVKA----------VSDVSSGKQVRGYVKGVISED-VLSHVEVVR 207
Query: 235 LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 294
LS I+ L+L+ + L +R G P+ Q A + + + EL+ L L ++K+ SN
Sbjct: 208 LSKKIKSGLRLDDHKSRLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSN 267
Query: 295 IRLVISIAKNYQGAGMNLQDLVQ 317
+RLV+SIA+ Y G + DLVQ
Sbjct: 268 VRLVMSIAQRYDNLGAEMSDLVQ 290
>sp|Q03066|RPSC_NOSS1 RNA polymerase sigma-C factor OS=Nostoc sp. (strain PCC 7120 / UTEX
2576) GN=sigC PE=3 SV=2
Length = 416
Score = 54.7 bits (130), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 39/125 (31%), Positives = 58/125 (46%), Gaps = 27/125 (21%)
Query: 215 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ- 273
RYL+ R++ AN Q L L ++E L+ G P+ +WAA AG++
Sbjct: 89 RYLKL-----RIVLANAVKQGDEVATPYLHLIEVQERLASELGHRPSLERWAATAGINLC 143
Query: 274 ---------------------RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNL 312
EL + + G+ K+ MI +N+RLV+S+AK YQ G+ L
Sbjct: 144 DLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLEL 203
Query: 313 QDLVQ 317
DLVQ
Sbjct: 204 LDLVQ 208
>sp|P77994|RPOD_THEMA RNA polymerase sigma factor RpoD OS=Thermotoga maritima (strain
ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=rpoD PE=1
SV=3
Length = 399
Score = 53.1 bits (126), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 34/46 (73%), Gaps = 1/46 (2%)
Query: 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+REL RR G K+K+ITSN+RLV+SIAK Y G G++ QDL+Q
Sbjct: 141 ERELARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQ 186
>sp|Q59996|RPSC_SYNY3 Probable RNA polymerase sigma-C factor OS=Synechocystis sp. (strain
PCC 6803 / Kazusa) GN=sigC PE=3 SV=1
Length = 404
Score = 52.0 bits (123), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 32/53 (60%)
Query: 265 WAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
WA AG+ EL GI K MI +N+RLV+S+AK YQ G+ L DL+Q
Sbjct: 144 WAELAGLTVEELENIEKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDLIQ 196
>sp|P74565|RPOD_SYNY3 RNA polymerase sigma factor RpoD OS=Synechocystis sp. (strain PCC
6803 / Kazusa) GN=rpoD PE=3 SV=1
Length = 425
Score = 48.5 bits (114), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 19/32 (59%), Positives = 25/32 (78%)
Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
KDKM+ SN+RLV+SIAK Y G++ QDL+Q
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 220
Score = 34.7 bits (78), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 193 KSGSTSRRKRPSVQEVDYS-DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV 251
K + ++ +V++ Y+ D +R RLL A EE++L+ I DLL+LE +R+
Sbjct: 51 KEKKVRKIRKDAVKKKPYTEDSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDN 110
Query: 252 LSERCGGSPTFAQWA 266
L+ + P+ +W
Sbjct: 111 LTLQLERQPSELEWG 125
>sp|P27785|RPOD_STRAU RNA polymerase sigma factor RpoD OS=Streptomyces aureofaciens
GN=rpoD PE=3 SV=1
Length = 317
Score = 48.1 bits (113), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 35/92 (38%), Positives = 51/92 (55%), Gaps = 13/92 (14%)
Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
LLTA EE+ L+ ++ L E E+ GG+ A + VD L R + G +
Sbjct: 33 LLTAAEEVDLARRVEAGLFAE-------EKLGGA---ADLDSQLAVD---LDRLVVMGRM 79
Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
K ++I SN+RLV+S+AK Y G G+ + DLVQ
Sbjct: 80 AKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQ 111
>sp|Q9ZSL6|SIGD_ARATH RNA polymerase sigma factor sigD, chloroplastic OS=Arabidopsis
thaliana GN=SIGD PE=2 SV=1
Length = 419
Score = 45.4 bits (106), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 36/101 (35%), Positives = 49/101 (48%), Gaps = 13/101 (12%)
Query: 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281
S S L+ EE+QL +++ KLE L G S + + R ++R
Sbjct: 118 SRSGFLSRLEEVQLCLYLKEGAKLENL--------GTSVEENEMVSVLLASGRGKKKRSA 169
Query: 282 YGILCKDKMITSNI-----RLVISIAKNYQGAGMNLQDLVQ 317
ILC+ K I RLV+SIA YQG G+NLQDL+Q
Sbjct: 170 NEILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQ 210
>sp|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis
GN=rpoD PE=1 SV=1
Length = 528
Score = 45.4 bits (106), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 9/92 (9%)
Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
LL A EE++L+ I+ L L LSER P +R++ G
Sbjct: 240 LLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP---------AAQRRDMMWICRDGDR 290
Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
K+ ++ +N+RLV+S+AK Y G GM DL+Q
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQ 322
>sp|P0A603|RPOD_MYCBO RNA polymerase sigma factor RpoD OS=Mycobacterium bovis (strain
ATCC BAA-935 / AF2122/97) GN=rpoD PE=3 SV=1
Length = 528
Score = 45.4 bits (106), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 9/92 (9%)
Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
LL A EE++L+ I+ L L LSER P +R++ G
Sbjct: 240 LLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP---------AAQRRDMMWICRDGDR 290
Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
K+ ++ +N+RLV+S+AK Y G GM DL+Q
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQ 322
>sp|Q31QR8|RPOD4_SYNE7 RNA polymerase sigma factor rpoD4 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD4 PE=3 SV=1
Length = 311
Score = 45.4 bits (106), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 39/119 (32%), Positives = 57/119 (47%), Gaps = 19/119 (15%)
Query: 199 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 258
RR + E SD + + ++ LLTA EE++LS +Q ++ L L
Sbjct: 6 RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMAL------LENPDAE 59
Query: 259 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
S + Q AG QR K KM+ +N+RLV+S+AK YQ G+ L DL+Q
Sbjct: 60 SNSENQAVLQAG--QR-----------AKTKMLKANLRLVVSVAKKYQNQGLELLDLIQ 105
>sp|P0CZ15|RPOD_RHOCA RNA polymerase sigma factor rpoD OS=Rhodobacter capsulatus GN=rpoD
PE=2 SV=1
Length = 674
Score = 43.5 bits (101), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 262 FAQWAAAAGVDQRELRRRLNY-------GILCKDKMITSNIRLVISIAKNYQGAGMNLQD 314
AQ GVD E RR +N K +M+ +N+RLVISIAK Y G+ D
Sbjct: 405 MAQVGQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 464
Query: 315 LVQ 317
L+Q
Sbjct: 465 LIQ 467
>sp|P18182|HRDA_STRCO RNA polymerase principal sigma factor HrdA OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdA
PE=3 SV=2
Length = 396
Score = 43.5 bits (101), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 26/35 (74%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
G L K ++I +N+RLV+S+AK Y G G+ + DLVQ
Sbjct: 156 GRLAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQ 190
>sp|D5AQI9|RPOD_RHOCB RNA polymerase sigma factor rpoD OS=Rhodobacter capsulatus (strain
ATCC BAA-309 / NBRC 16581 / SB1003) GN=rpoD PE=3 SV=1
Length = 674
Score = 43.5 bits (101), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 262 FAQWAAAAGVDQRELRRRLNY-------GILCKDKMITSNIRLVISIAKNYQGAGMNLQD 314
AQ GVD E RR +N K +M+ +N+RLVISIAK Y G+ D
Sbjct: 405 MAQVGQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 464
Query: 315 LVQ 317
L+Q
Sbjct: 465 LIQ 467
>sp|Q9Z7F0|RPOD_CHLPN RNA polymerase sigma factor RpoD OS=Chlamydia pneumoniae GN=rpoD
PE=3 SV=1
Length = 572
Score = 43.1 bits (100), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 30/46 (65%)
Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
D R L+R ++ K +M+ SN+RLVISIAK Y G++ DL+Q
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQ 348
>sp|P56835|RPOD_CHLMU RNA polymerase sigma factor RpoD OS=Chlamydia muridarum (strain
MoPn / Nigg) GN=rpoD PE=3 SV=1
Length = 571
Score = 43.1 bits (100), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 30/46 (65%)
Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
D R L+R ++ K +M+ SN+RLVISIAK Y G++ DL+Q
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQ 348
>sp|P18333|RPOD_CHLTR RNA polymerase sigma factor RpoD OS=Chlamydia trachomatis (strain
D/UW-3/Cx) GN=rpoD PE=3 SV=2
Length = 571
Score = 42.7 bits (99), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 30/46 (65%)
Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
D R L+R ++ K +M+ SN+RLVISIAK Y G++ DL+Q
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQ 348
>sp|P52329|RPOD_ENTFA RNA polymerase sigma factor RpoD OS=Enterococcus faecalis (strain
ATCC 700802 / V583) GN=rpoD PE=3 SV=2
Length = 368
Score = 42.4 bits (98), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 38/138 (27%), Positives = 55/138 (39%), Gaps = 52/138 (37%)
Query: 180 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 239
+ AEKA A +S +G V +DP+R +LLTA EE++L+ I
Sbjct: 77 KEAEKAQAEDLSAPTG------------VKINDPVRMYLKEIGRVQLLTAAEEVELALKI 124
Query: 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299
+ EG +E K ++ +N+RLV+
Sbjct: 125 E-----EGDQE-----------------------------------AKQRLAEANLRLVV 144
Query: 300 SIAKNYQGAGMNLQDLVQ 317
SIAK Y G GM DL+Q
Sbjct: 145 SIAKRYVGRGMQFLDLIQ 162
>sp|O83506|RPOD_TREPA RNA polymerase sigma factor RpoD OS=Treponema pallidum (strain
Nichols) GN=rpoD PE=3 SV=1
Length = 611
Score = 42.0 bits (97), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
KDK+I +N+RLV+SIAK Y G+ DLVQ
Sbjct: 374 KDKLINANLRLVVSIAKKYTNRGLLFFDLVQ 404
>sp|Q9PDM9|RPOD_XYLFA RNA polymerase sigma factor RpoD OS=Xylella fastidiosa (strain
9a5c) GN=rpoD PE=3 SV=1
Length = 618
Score = 42.0 bits (97), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 272 DQRELRRRLNYG----ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
D +E+ R + YG K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 361 DIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 410
>sp|Q87DT7|RPOD_XYLFT RNA polymerase sigma factor RpoD OS=Xylella fastidiosa (strain
Temecula1 / ATCC 700964) GN=rpoD PE=3 SV=1
Length = 618
Score = 42.0 bits (97), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 4/50 (8%)
Query: 272 DQRELRRRLNYG----ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
D +E+ R + YG K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 361 DIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 410
>sp|P18184|HRDC_STRCO RNA polymerase principal sigma factor HrdC OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdC
PE=3 SV=1
Length = 339
Score = 41.6 bits (96), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 30/96 (31%), Positives = 51/96 (53%), Gaps = 9/96 (9%)
Query: 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281
++ LLTA +E++L+ I+ ++ RE L G P A +R L ++
Sbjct: 47 GATPLLTAEDEVRLATRIEAGVRA---REELETADTGEP------APTPRRRRTLEETVH 97
Query: 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
G KD M+ +N+RLV+S+AK + G+ L D++Q
Sbjct: 98 DGQEAKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQ 133
>sp|Q83BB6|RPOD_COXBU RNA polymerase sigma factor RpoD OS=Coxiella burnetii (strain RSA
493 / Nine Mile phase I) GN=rpoD PE=1 SV=1
Length = 698
Score = 40.8 bits (94), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+E+ RR+ G K +MI +N+RLVISIAK Y G+ DL+Q
Sbjct: 442 KEINRRVAIGEAKSRRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQ 489
>sp|P52323|RPOD_BORBU RNA polymerase sigma factor RpoD OS=Borrelia burgdorferi (strain
ATCC 35210 / B31 / CIP 102532 / DSM 4680) GN=rpoD PE=3
SV=2
Length = 631
Score = 40.8 bits (94), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 24/31 (77%)
Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
KD++I +N+RLV+SIAK Y G++ DLVQ
Sbjct: 392 KDQLIKANLRLVVSIAKKYANRGLHFFDLVQ 422
>sp|P52327|RPOD_PSEPU RNA polymerase sigma factor RpoD OS=Pseudomonas putida GN=rpoD PE=3
SV=1
Length = 614
Score = 40.4 bits (93), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+E+ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 360 KEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 407
>sp|Q59914|HRDD_STRGR RNA polymerase principal sigma factor HrdD OS=Streptomyces griseus
GN=hrdD PE=3 SV=1
Length = 332
Score = 40.4 bits (93), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 268 AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+AG + EL + G KD I SN+RLV+++A+ Y +G+ L DL+Q
Sbjct: 78 SAGASREELEALVAEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQ 127
>sp|P18183|HRDB_STRCO RNA polymerase principal sigma factor HrdB OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdB
PE=3 SV=2
Length = 511
Score = 40.4 bits (93), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+REL G K+ ++ +N+RLV+S+AK Y G GM DL+Q
Sbjct: 261 KRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQ 305
>sp|P33118|RPSB_CORDI RNA polymerase sigma factor SigB OS=Corynebacterium diphtheriae
(strain ATCC 700971 / NCTC 13129 / Biotype gravis)
GN=sigB PE=3 SV=2
Length = 329
Score = 40.4 bits (93), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 30/45 (66%)
Query: 273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+R+L+ + G + ++ +N+RLV+S+AK Y G GM L DL+Q
Sbjct: 79 KRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 123
>sp|Q59753|RPOD_RHIME RNA polymerase sigma factor RpoD OS=Rhizobium meliloti (strain
1021) GN=rpoD PE=3 SV=1
Length = 684
Score = 40.4 bits (93), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 23/33 (69%)
Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+ K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 445 IAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 477
>sp|P50511|RP32_VIBCH RNA polymerase sigma-32 factor OS=Vibrio cholerae serotype O1
(strain ATCC 39315 / El Tor Inaba N16961) GN=rpoH PE=3
SV=2
Length = 286
Score = 40.4 bits (93), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 272 DQRELRRRLNY--GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
++REL RL+Y I +I S++R V+ +A+ Y G G+ + DLVQ
Sbjct: 33 EERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPMADLVQ 80
>sp|Q2K619|RPOD_RHIEC RNA polymerase sigma factor rpoD OS=Rhizobium etli (strain CFN 42 /
ATCC 51251) GN=sigA PE=1 SV=1
Length = 685
Score = 40.0 bits (92), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 23/33 (69%)
Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+ K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 446 IAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 478
>sp|P33452|RPOD_AGRT5 RNA polymerase sigma factor RpoD OS=Agrobacterium tumefaciens
(strain C58 / ATCC 33970) GN=rpoD PE=3 SV=2
Length = 684
Score = 40.0 bits (92), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 23/33 (69%)
Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+ K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 445 IAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 477
>sp|P77951|HRDB_STRGR RNA polymerase principal sigma factor HrdB OS=Streptomyces griseus
GN=hrdB PE=1 SV=1
Length = 514
Score = 40.0 bits (92), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+REL G K+ ++ +N+RLV+S+AK Y G GM DL+Q
Sbjct: 264 KRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQ 308
>sp|P0A2E3|RPOD_SALTY RNA polymerase sigma factor RpoD OS=Salmonella typhimurium (strain
LT2 / SGSC1412 / ATCC 700720) GN=rpoD PE=3 SV=1
Length = 615
Score = 39.7 bits (91), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 361 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 408
>sp|P0A2E4|RPOD_SALTI RNA polymerase sigma factor RpoD OS=Salmonella typhi GN=rpoD PE=3
SV=1
Length = 615
Score = 39.7 bits (91), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 361 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 408
>sp|Q8PG33|RPOD_XANAC RNA polymerase sigma factor RpoD OS=Xanthomonas axonopodis pv.
citri (strain 306) GN=rpoD PE=3 SV=1
Length = 625
Score = 39.7 bits (91), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+E+ R + YG K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 370 KEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 417
>sp|Q9ZNX9|SIGE_ARATH RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
OS=Arabidopsis thaliana GN=SIGE PE=1 SV=1
Length = 517
Score = 39.7 bits (91), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 3/95 (3%)
Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
+L++ E L +Q + L +++VL + G P A+ A + E+++++ G
Sbjct: 219 VLSSTEHAWLFKLMQPMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRA 278
Query: 286 CKDKMITSNIRLVISIAKNYQGA---GMNLQDLVQ 317
++K+I N+RLV+ + Y G QDL Q
Sbjct: 279 ARNKLIKHNLRLVLFVMNKYFHEFTNGPKFQDLCQ 313
>sp|O24744|RPOD_SHEVD RNA polymerase sigma factor RpoD OS=Shewanella violacea (strain JCM
10179 / CIP 106290 / LMG 19151 / DSS12) GN=rpoD PE=3
SV=1
Length = 614
Score = 39.7 bits (91), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 360 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 407
>sp|Q8CP24|RPOD_STAES RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 12228) GN=rpoD PE=3 SV=1
Length = 368
Score = 39.7 bits (91), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 275 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+Q
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQ 162
>sp|Q5HNY7|RPOD_STAEQ RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 35984 / RP62A) GN=rpoD PE=3 SV=1
Length = 368
Score = 39.7 bits (91), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 275 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+Q
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQ 162
>sp|P00579|RPOD_ECOLI RNA polymerase sigma factor RpoD OS=Escherichia coli (strain K12)
GN=rpoD PE=1 SV=2
Length = 613
Score = 39.7 bits (91), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 4/48 (8%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+Q
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406
>sp|Q60012|HRDD_STRVF RNA polymerase principal sigma factor HrdD OS=Streptomyces
viridifaciens GN=hrdD PE=3 SV=1
Length = 332
Score = 39.7 bits (91), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 29/43 (67%)
Query: 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
EL+ ++ G KD I SN+RLV+++A+ Y +G+ L DL+Q
Sbjct: 85 ELQALVDAGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQ 127
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.311 0.123 0.326
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 101,850,099
Number of Sequences: 539616
Number of extensions: 3667586
Number of successful extensions: 14153
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 145
Number of HSP's successfully gapped in prelim test: 176
Number of HSP's that attempted gapping in prelim test: 13733
Number of HSP's gapped (non-prelim): 516
length of query: 328
length of database: 191,569,459
effective HSP length: 118
effective length of query: 210
effective length of database: 127,894,771
effective search space: 26857901910
effective search space used: 26857901910
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (28.1 bits)